Im fairly new to all grain brewing ...8 five gal batches so far so this might be a really silly question.
I recently purchased a PolarWare 10 gal brew pot complete with stainless steel false bottom.
The false bottom sits above the outlet so I have rigged a drain pipe to reach to the middle of the pot bottom. The bottom of the drain pipe sits quite close to the bottom of the pot, so by siphoning through the attached spigott, I get most the liquid out of the pot.
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That could be part of your problem. Your L/G ratio is thinner so your gravity readings are lower. I would calculate the original gravity that you expect, then choose a L/G and mash with that amount of water. You may be adding make up water to fill the kettle to compensate for the loss in the mash tun (over sparging).

Another possable problem is temperature. Did you pre-heat the mash tun before mashing and calculate your strike heat per the grain temperature? Each of these could lower the mash temperature so you may not get maximum conversion. I would check the mash temperature at the beginning and at mash out. Your pot will also loose more heat than the cooler.

I would also download a trial copy of Promash. It has a good water calculator. Using it can get you real close to the numbers that you want to hit.